[gmx-users] Flat-bottom potential SEGFAULT

[Erik Marklund]

Hi,

>From what I have observed so far this appears to be a cluster configuration issue rather than a gromacs error. Thanks for your input.

Kind regards,
Erik

On 29 Mar 2016, at 15:14, Erik Marklund <erik.marklund at chem.ox.ac.uk<mailto:erik.marklund at chem.ox.ac.uk>> wrote:


On 28 Mar 2016, at 01:52, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:



On 3/26/16 12:47 PM, Erik Marklund wrote:
Dear dynamicists,

I am using flat bottom potentials to prevent water molecules from evaporating from a droplet in vacuum. The manual suggests this is pretty straightforward, but we run into a segfault with our approach. Having never used flat-bottom potentials before, chances are we are doing something wrong without realising it. Let me describe what we do and perhaps you can tell me where things go wrong.

We make our own copy of tip3p.itp, in which we put a [ position_restraints ] directive for the OW1, HW2, and HW3 atoms:
[ position_restraints ]
; id func_type    g   r  k
1    2            1   10 1000
2    2            1   10 1000
3    2            1   10 1000

We then create a new gro-file, where we move all water atoms in the middle of the box. This is to be used for reference coordinates in the next step.

We run grompp, where we provide the new gro file using the -r flag.

We launch mdrun, which segfaults. If we prepare the system without the -r flag in the previous step everything runs fins, but the reference point for the flat-bottom potential is presumably wrong.

Where might the error be?


I just did this with a toy system of a single water molecule and it worked quite well.  What version of GROMACS are you using?  Does a simple test like I did work?

-Justin

Hi,

Forgot to mention the version. It is 5.1.1. Will run some simple tests like yours and get back with more info.

Kind regards,
Erik


--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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